The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Open accessAbstract
A translational medicine pipeline is described where human gut microbial communities and diets are re-created in gnotobiotic mice and the impact on microbe and host is defined using metagenomics.
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In the citing paper
“The majority of studies in humans and mice rely on faecal samples, which provide some representation of what is occurring throughout the digestive tract”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [120]
In the citing paper
“aspects of microbial communities and host responses that are specific to the small intestine might be obscured by faecal sampling119,120.”
From Diet–microbiota interactions as moderators of human metabolism (2016) · cites this paper as [120]
In the citing paper
“Our study corroborates previous studies showing an association between altered diets and an increase in Erysipelotrichi and Allobaculum, but various effects are shown for fat-enriched diets 29, 30, 31, 32.”
From The composition of the gut microbiota shapes the colon mucus barrier (2015) · cites this paper as [32]
In the citing paper
“Similar to the Western diet, high-fat diets in animal studies reproducibly change gut microbial community structure, decreasing the overall microbiota diversity and beneficial bacteria (e.g., A. muciniphila, Bifidobacterium, Lactobacillus, and Lactococcus) and increasing the Firmicutes:Bacteroidetes ratio and the abundance of Enterobacteriales, Clostridium cluster XVIa, Mollicutes, and B. wadswort”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [206]
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Citations
Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Self-citationThe RAST Server: Rapid Annotations using Subsystems Technology
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T. L., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-75 · Cited by 11,893
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Self-citationA core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Self-citationObesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
Self-citationThe Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., & Henrissat, B. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn663 · Cited by 6,108
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091
Self-citationThe KEGG resource for deciphering the genome
Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,120
Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953
Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.015 · Cited by 2,915
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Quercetin metabolism by fecal microbiota from healthy elderly human subjects
Tamura, M., Hoshi, C., Kobori, M., Takahashi, S., Tomita, J., Nishimura, M., & Nishihira, J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0188271 · Cited by 60
The Gut Microbiome, Energy Homeostasis, and Implications for Hypertension
Riedl, R. A., Atkinson, S. N., Burnett, C. M. L., Grobe, J. L., & Kirby, J. R. (2017) · Current Hypertension Reports · doi:10.1007/s11906-017-0721-6 · Cited by 58
Genetic modification of iron metabolism in mice affects the gut microbiota
Buhnik-Rosenblau, K., Moshe-Belizowski, S., Danin-Poleg, Y., & Meyron-Holtz, E. G. (2012) · BioMetals · doi:10.1007/s10534-012-9555-5 · Cited by 53
Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition
Herman, D. R., Rhoades, N., Mercado, J., Argueta, P., Lopez, U., & Flores, G. E. (2020) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2019.07.024 · Cited by 50
Holm, J. B., Rønnevik, A., Tastesen, H. S., Fjære, E., Fauske, K. R., Liisberg, U., Madsen, L., Kristiansen, K., & Liaset, B. (2016) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2015.12.017 · Cited by 45
Ren, Z., Xu, Y., Li, T., Sun, W., Tang, Z., Wang, Y., Zhou, K., Li, J., Ding, Q., Liang, K., et al. (2022) · Animal Nutrition · doi:10.1016/j.aninu.2022.06.009 · Cited by 44
“High-carbohydrate and high-fiber diets increase the expression of butyrate-producing related genes in the gut microbiota, whereas HFD can reverse these positive effects at the transcriptional level (Turnbaugh et al., 2009; Wu et al., 2011; Qin et al., 2012; Koh et al., 2016; Zhao et al., 2018).”
BackgroundMicrobiome: paediatricians’ perspective
Arora, S., Dewan, P., & Gupta, P. (2015) · Indian Journal of Medical Research · doi:10.4103/0971-5916.171275 · Cited by 39
Mirror, mirror on the wall: which microbiomes will help heal them all?
Nayak, R. R., & Turnbaugh, P. J. (2016) · BMC Medicine · doi:10.1186/s12916-016-0622-6 · Cited by 36
“Additional causal insights would need to come from germ-free, or gnotobiotic, mouse models with microbiomes that are derived from human donors [47].”
BackgroundSelf-citationThe primary biological network of Bifidobacterium in the gut
Luo, J., Li, Y., Xie, J., Gao, L., Liu, L., Ou, S., Chen, L., & Peng, X. (2018) · FEMS Microbiology Letters · doi:10.1093/femsle/fny057 · Cited by 36
“Gut microbiota in the biological network alternates owing to various factors, such as age, diet, pathological states and medication, and diet being the major factor among them (Turnbaugh et al. 2009; Sanchez et al. 2013).”
BackgroundCuervo, A., Hevia, A., López, P., Suárez, A., Diaz, C., Sánchez, B., Margolles, A., & González, S. (2016) · Food & Function · doi:10.1039/c5fo00853k · Cited by 32
Nilsson, A., Johansson-Boll, E., Sandberg, J., & Björck, I. (2016) · Clinical Nutrition ESPEN · doi:10.1016/j.clnesp.2016.06.006 · Cited by 30
Gut microbiome response to short‐term dietary interventions in reactive hypoglycemia subjects
Quercia, S., Turroni, S., Fiori, J., Soverini, M., Rampelli, S., Biagi, E., Castagnetti, A., Consolandi, C., Severgnini, M., Pianesi, M., et al. (2017) · Diabetes/Metabolism Research and Reviews · doi:10.1002/dmrr.2927 · Cited by 27
Gut microbiota in multiple sclerosis and animal models
Schumacher, S. M., Doyle, W. J., Hill, K., & Ochoa‐Repáraz, J. (2025) · The FEBS Journal · doi:10.1111/febs.17161 · Cited by 21
Parenteral Nutrition, Inflammatory Bowel Disease, and Gut Barrier: An Intricate Plot
Covello, C., Becherucci, G., Di Vincenzo, F., Del Gaudio, A., Pizzoferrato, M., Cammarota, G., Gasbarrini, A., Scaldaferri, F., & Mentella, M. C. (2024) · Nutrients · doi:10.3390/nu16142288 · Cited by 21
“The term “dysbiosis” is used to describe a state characterized by decreased microbial variety and diversity, alterations in the Firmicutes/Bacteroidetes ratio, proliferation of lipopolysaccharide-producing Gram-negative Proteobacteria (LPS), and heightened intestinal permeability [58–61].”
BackgroundAn overview of the microbiome and the effects of antibiotics
Taggart, H., & Bergstrom, L. (2014) · The Journal for Nurse Practitioners · doi:10.1016/j.nurpra.2014.05.005 · Cited by 14
“These Western dietefed mice also developed adiposity within 2 weeks of switching diets compared with control mice and transmitted this trait to other gnotobiotic mice through fecal microbiota transplantation performed by the investigators.(35)”
BackgroundEarly Childhood Obesity Prevention Policies
(2011) · doi:10.17226/13124 · Cited by 452
The Gastrointestinal Tract and Its Microflora
Aimutis, W. R., & Polzin, K. (2010) · Nondigestible Carbohydrates and Digestive Health · doi:10.1002/9780470958186.ch2 · Cited by 1
Wang, H.-X., & Wang, Y.-P. (2016) · Chinese Medical Journal · doi:10.4103/0366-6999.190667 · Cited by 546
Metadata
- Authors
- Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I.
- Affiliations
- Washington University in St. Louis (US)
- University of Colorado Boulder (US)
- Corresponding author
- Gordon, Jeffrey I.
- ORCID
- Venue
- Science Translational Medicine
- Published
- 2009-11-11
- Volume
- 1
- Issue
- 6
- Pages
- 6ra14-6ra14
- ISSN
- 1946-6234 (ISSN-L)
- 1946-6242
- PMC
- PMC2894525
- OpenAlex
- W2136552678
- Cited by
- 3,058
- References
- 27
- Citations by year
- 2026: 71 · 2025: 112 · 2024: 140 · 2023: 158 · 2022: 201 · 2021: 251 · 2020: 269 · 2019: 288 · 2018: 248 · 2017: 246 · 2016: 237 · 2015: 198 · 2014: 183 · 2013: 173 · 2012: 131
- FWCI
- 37.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science Translational Medicine (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Crohn's and Colitis Foundation
- National Institute of Diabetes and Digestive and Kidney Diseases (DK 70977, R01DK070977)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Keywords
- gut microbiota, diet, fecal microbiota transplantation, Western diet, high-fat high-sugar diet, bacterial colonization, intergenerational transmission, adiposity, metabolic pathways, germ-free mice, 16S rRNA gene sequences
- MeSH terms
- Animals, Bacteria, Diet, Energy Metabolism, Germ-Free Life, Humans, Intestines, Male, Mice, Inbred C57BL, Molecular Sequence Data, RNA, Ribosomal, 16S, Genomics, Adiposity, Mice
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